Haptophyta

Cells of Haptophyceae species normally possess one or two chloroplasts containing thylakoids stacked in three to form lamellae. There is no girdle lamella. Spindle-shaped pyrenoids are commonly immersed within the chloroplast, penetrated by one or a few pairs of thylakoids, but in some genera they bulge from the inner face of the organelle. Both the chloroplast and the pyrenoid are surrounded by endoplasmic reticulum confluent with the nuclear envelope, the nucleus itself lying close to the chloroplast. Chlorophylls a, c₁ and c₂ and in some genera also c₃ are found in the thylakoidal membranes together with carotenes, such as β-carotene, and xanthophylls, the most commonly occurring being fucoxanthin. DNA is organized into numerous nucleoids scattered throughout the chloroplast.

Cryptophyta

The chloroplasts of these algae, one or two per cell, are unusual in both their pigment composition and ultrastructure. Four membranes enclose these organelles: the inner pair forms the plastid envelope and the outer pair forms the plastid endoplasmic reticulum. This four-membrane configuration is common in chlorophyll c-containing algae. An expanded space is present between the plastid endoplasmic reticulum and the plastid envelope on its inward face. This compartment contains 80S ribosomes, starch grains, and the nucleomorph. Thylakoids inside the chloroplast are typically in pairs, although single thylakoids as well as large stacks have been also observed, with no girdle lamella. A pyrenoid is present, projecting from the inner side of the chloroplast. Cryptomonads are characterized by the presence of chlorophylls a and c₂; phycoerythrin, phycocyanin, and allophycocyanin; carotenes, and several xanthophylls.

The phycobiliproteins differ from those in the red algae and cyanobacteria, because they are of lower molecular weight, and do not aggregate to form discrete phycobilisomes, being localized within the lumen of the thylakoids. DNA is organized into numerous nucleoids scattered throughout the chloroplast.

Dinophyta

Chloroplasts may be present or absent in these algae, depending on the nutritional regimen. When present, they are characterized by triple-membrane envelopes not connected with the endoplasmic reticulum; thylakoids are usually in group of three, unappressed, and girdle lamellae are generally absent. Pyrenoids show various types, stalked or embedded within the chloroplast. The pigment assortment includes chlorophylls a and c₂, β-carotene, and several xanthophylls, among which is piridinin. DNA is organized into numerous nodules scattered throughout the chloroplast. This description corresponds to the most important dinoflagellates plastid, the peridinin-type plastid. About 50% of dinoflagellates with plastids acquired them from a variety of photosynthetic eukaryotes by endosymbiosis. Those containing three-membrane, peridinincontaining plastids, such as Amphidinium carterae, probably derived from the red lineage by secondary endosymbiosis, that is, through the uptake of primary plastid-containing endosymbiont. Other groups of dinoflagellates have plastids derived from a tertiary endosymbiotic event, that is, the uptake of a secondary plastid-containing endosymbiont.

Tertiary plastids are present in the toxic genus Dinophysis, characterized by two-membrane, cryptophyte-derived plastids, in other important species (Karenia sp., Gyrodinium aureolum, and Gymnodinium galatheanum) with fucoxanthin as accessory pigment, which possess haptophyte-derived plastids surrounded by two or four membranes, and in Kryptoperidinium sp. and close relatives, which have a five-membrane, heterokontophyte-derived (diatom) plastid that includes a diatom nucleus of unknown complexity. Another case is that of Gymnodinium acidotum, characterized by a cryptophyte endosymbiont, which may or may not represent a permanent endosymbiosis, because the endosymbiont may be acquired as prey and retained for long periods of time, but not kept permanently.

A serial secondary endosymbiosis (the uptake of a new primary plastid-containing endosymbiont) occurred in Lepidodinium sp. and its close relatives, in which the peridinin plastid has apparently been replaced by a secondary plastid derived probably from a prasinophycean alga (Chlorophyta) and surrounded by two membranes. This dinoflagellate also has external scales atypical for its division, but closely resembling those of Prasinophyceae, suggesting that Lepidodinium expresses genes for scale formation acquired from its endosimbiont. Also in Noctiluca sp. a Prasinophyceae endosymbiont has been observed.